class: center, middle, inverse, title-slide # Exploring the complexity of ecological networks using SVD entropy ###
Tanya Strydom, Gullio V. Dalla Riva & Timothée Poisot
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@TanyaS_08
@TanyaS08
--- class: center, middle Presentation created using **{xaringan}** (the **robot** theme) Slides available at [https://tanyas08.github.io/Talks/2020_Dec_TUKS/index.html#1](https://tanyas08.github.io/Talks/2020_Dec_TUKS/index.html#1) --- # The Backstory .center[species interaction networks 🕸 + fancy maths 🧮 | FAIR & Open Science ⚖️ | part-time doodler 🎨 | warm beverage fan ☕] -- .center[ <br> Participant of the 5th [Plant Functional Traits Course](https://plantfunctionaltraitscourses.w.uib.no/) Placed a lot of focus on doing reproducible science <br> Inspired [this](https://doi.org/10.1002/ece3.7009) manuscript on how we can incorporate teaching FAIR and Open Science in student training ] -- <span style="margin: 0; position: absolute; top: 31%; left: 15%;"> <img src="data:image/png;base64,#img/NextGen.png" width="85%" /></span> -- <span style="margin: 0; position: absolute; top: 31%; left: 27%;"> <img src="data:image/png;base64,#img/Panel2.png" width="67%" /></span> --- # What is Open Science? .center[*A global movement to promote integrity, repeatability, and transparency across all aspects of scientific research*] -- .pull-left[ **Which includes:** - Open access to publications - Open access to data - Open source code and data handling ] -- <span style="margin-left:-47%; position: absolute; top: 63%"><img src="data:image/png;base64,#img/TheWay.jpeg" width="58%" /></span> --- # Make your Science FAIR .center[***F**indable, **A**ccessible, **I**nteroperable and **R**eproducible*] --- # Where to Start Though? .footnote[[*] Respecting data sharing restrictions and embargoes] .left-column[data lifecycle.png] .right-column[ - Think about how you enter your data * Follow data and metadata standards (e.g. [DarwinCore](https://www.tdwg.org/)) * Document it (e.g. README file) think of this as an extensive methods section - Document data processing and analysis * Use code-based workflows * Annotate said code - Archive data in an accessible way * Make as open and findable as possible<sup>*</sup> e.g. a data statement and link to archive/repository * Use non-propriety file formats e.g. .csv/.txt * Include **all** documentation - Do some of your own research ] --- class: inverse, middle, center background-image: url(data:image/png;base64,#https://d33wubrfki0l68.cloudfront.net/62bcc8535a06077094ca3c29c383e37ad7334311/a263f/assets/img/logo.svg) background-position: bottom background-size: 20% # 1. Scripting changes --- background-image: url(data:image/png;base64,#https://d33wubrfki0l68.cloudfront.net/62bcc8535a06077094ca3c29c383e37ad7334311/a263f/assets/img/logo.svg) background-position: bottom right background-size: 20% # Keep it Scripted Ultimately after inputting your data into a file<sup>*</sup> it should remain untouched and unchanged. .footnote[[*] Ideally using a non propriety format such as .csv or .txt] -- **What does that even mean?** -- - We want to keep `data_raw.csv` intact and end up with `data_clean.csv` on the other side -- **Why should I script it?** -- 1. It allows you (and others) to keep track of<br>what you changed 1. Document why you made the changes you<br>did (*sensu lato* a lab book) 1. Avoid the all to common `_cleaned`,<br>`_cleaned2` issue --- class: inverse, middle, center background-image: url(data:image/png;base64,#https://d33wubrfki0l68.cloudfront.net/62bcc8535a06077094ca3c29c383e37ad7334311/a263f/assets/img/logo.svg) background-position: bottom background-size: 20% # 2. Annotating code --- # Annotations save lives <sub style="font-size: medium;">(and time)</sub> Annotating your code by adding comments makes it easier for you (and others) to understand what or why you decided to do what you did -- .pull-left[ - Pseudocode can double up as annotations * Pseudocoding is a way of writing out your code in 'plain language' before you start coding it up - Detail specific changes or reasoning * Especially when cleaning or transforming data ] --- class: inverse, middle, center background-image: url(data:image/png;base64,#https://d33wubrfki0l68.cloudfront.net/62bcc8535a06077094ca3c29c383e37ad7334311/a263f/assets/img/logo.svg) background-position: bottom background-size: 20% # 3. Data Archiving <sub style="font-size: medium;">(with bonus version control)</sub> --- # Get with GitHub Think of GitHub as a google drive of sorts that you would keep your projects in - the only difference is that it has some bonus features. * **It's Open Access:** Like a social media profile that people can click on and explore it *i.e.* you can share and showcase your work/packages/projects<sup>*</sup>. + This is where your data/analyses can 'live' until needed. * **It has Version Control:** This means that every time you re-upload a file the older versions are saved (and can be recouped if needed). + You can do this [straight from RStudio](https://happygitwithr.com/rstudio-git-github.html) + This also facilitates collaboration in a big way (no more email chain!) * **It's Designed for Programming:** Aside form simple storage of files you can design [workflows](https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions) that run jobs depending on what happens in the repository. .footnote[[*] I find this also 'forces' me to make sure my code is readable/shareable] --- # A GitHub 'Primer' 1. GitHub is the 'norm' in the world of Open Source - so if you want to go open go with GitHub 1. [Happy Git and GitHub for the useR](https://happygitwithr.com) is a great starting point if you're interested + especially for installing Git on your device (it can be a bit confusing) 1. You can also have private repositories * So you can keep your work 'hidden' but still cash in on version control and easier collaborating 1. As university students you qualify for a [free pro account](https://education.github.com/pack) - *go for it it* --- # Other Ways to Open your Science +